In Group D, both NorthEast and Mumbai City FC finished with six points each, but the Guwahati side made the grade by virtue of their better head-to-head record.
Chennaiyin FC beat NorthEast United 4-2 in the second match in Group D.
Farshad Noor scored the solitary goal in Vasco da Gama.
The 21-year-old has penned a multi-year deal that keeps him at the club until 2025.
The 22-year-old has singed a four-year deal with the ISL finalists.
Gokulam Kerala that dominated the match with 69% possession was held 1-1 by Churchill.
Gokulam wasted no time in taking the game to their opponents, finding an early breakthrough in the second minute of the contest.
Gokulam Kerala skipper Sharif Mohammad scored the solitary goal of the match from the penalty spot early in the first half.
Both Gokulam and Churchill ended up tied with 29 points, but Gokulam emerged champions on head-to-head record.
The Malabarians have become the first team from Kerala to win the I-League title.